I didn't find a traditional way to fix the dup TrueClass, but I found a good enough way around it so I can develop locally without having to switch those paths each time.
In the guide for gh-pages to jekyll here: http://jekyllrb.com/docs/github-pages/
They specifically state to not have a trailing slash on your baseurl in your _config.yml. I found by not following their advice and using a trailing slash in _config.yml like so:
baseurl: /my-path/
I could have all my other links still use the {{ site.baseurl }} path just without the leading slash and use:
jekyll serve --baseurl '/' -w
So all my paths work just fine. Example:
<link rel="stylesheet" href="{{ site.baseurl }}css/sytle.css">
That way it works when I push up to gh-pages too.